the unlocks from safehouse, whther you go from sotry mode or contract sides, is all for contracts, the only reason you can see the unlocks on the story side, is because the screen the shows assassin skills youve unlocked, which is shared on both sides. But you can not cusomize single player weapons. You can test it if your not sure, do a mission where you use the silverballers, take off the silence, and dual upgrades, but you still get them in the mission